A Complicated Reunion
by TheCuriousConscious
Summary: During that time so many years ago, he had done the very same thing. So who is he to expect that he should, or will, be forgiven. For who is he? He's only a Medical Officer aboard the Enterprise, and him? A man, broken and torn apart, only to be filled with grief and rage. Which is the deadliest combination of all. Sherlock/John pairing. All those in Sherlock will be in the story.
1. Chapter 1

**This is my first attempt at this type of cross-over. If I have stolen somebody's story please forgive me because it was very much unintentional. Reviews are greatly appreciated for this story! Alright, as a heads up I'm going to start out from the cliché scene where Kirk and Spock are taking to Kahn behind the glass. Bear with me...I'm going to change some things...a lot I'm pretty sure *winces*, so again, hang in there. **

**I do not own Star Trek or anything of that nature, therefore everything in my story belongs to their rightful owners. {The Sherlock & Star Trek 'Verse}**

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"Why is there a man in that torpedo?" Kirk's voice devoid of anything but the want of an answer to the question. It quite effectively ripped the black clad man of is thoughts once his voice broke the silence.

"There are men and women in _all _those torpedoes Captain, I put them there." His voice dripped with boredom and yet he sat stiffly as if anticipating an attack, his presence contradicting itself as he made eye contact with the Captain. He allowed them a moment to glance to each other as his eyes flicked briefly open to the doors that softly hissed open. A flash of blue and blonde was all he caught before Kirk spoke up again.

"Who the hell are you?" The man in black simply fixed Kirk with a disapproving stare and remained stubbornly quite feeling as though the question was simple enough and did not deserve an answer. Until he gave in, his hand slowly clenching until he felt the small prick of his nails digging into the flesh of his palm.

"A remnant of a time long passed." He began, eyes becoming more unfocused on the present and more on the memories that he begrudgingly brought forth. "Genetically engineered to be superior, so as to lead others to peace in a world at war." He paused again the memory of his crew lined up before him with blank faces, waiting to be commanded before it faded into that of them sleeping in the cryogenice pods. "We were condemned, as criminals _forced_ into exile. For centuries we slept," He stopped momentarily riveting his attention on Spock. "Hoping that when we awoke things would be, different." Determination filtered into his eyes as he spoke faster, and with more hostility than before. "But as a result of the destruction of Vulcan, _your _Starfleet began to aggressively search distant quadrants of space my ship was found adrift I alone, was revived." The sound of a small item dropping upon metal distracted him from his company for a moment as he searched for the source, before Kirk began to speak.

"I looked up John Harrison." The Captain began with conviction. "Until a year ago he didn't _exist._" There was another clatter behind them that almost cause Kirk to turn around but the captive before him had become impatient and restless, standing up and beginning to pace.

"John Harrison was a fiction created the moment I was awoken by your Admiral Marcus to help him advance his, cause." Stalking towards the Captain the man had a lethal grace that may have awed, even intimidated the Captain had they not been in this particular situation. "A smokescreen to conceal my true identity. My name, is, _Khan_." He spat, a quality of harsh and quiet that made Kirk wonder if he should have known about him before this moment.

A crash resounded from behind them and this time Kirk did respond, "Doctor! If you cannot control yourself than please remove yourself!" he all but shouted, his nerves too frayed to ask politely. The man in question, the same one that had entered only a few moment prior Kahn noted, ducked his head murmuring his apologies, too embarrassed to speak up. The Captain gave him a brisk nod to and turned back around making the Doctor run a hand through his hair as he let out a breath before returning to his work.

"Why would a Starfleet Admiral, ask a three hundred year old man for help?" Kirk questioned.

"Because I am, better." Kahn hissed.

"At what?"

"_Everything. _Alexander Marcus needed to respond to an uncivilized threat in a civilized time," His bearing became restless and impatient once again for the longer he spoke, shifting his weight he started to turn his back on the Captain and his First Officer. "And for that he needed a warriors' mind, _my _mind. To design weapons, and warships-" He was cut off as Spock interrupted him disbelieving.

"You are suggesting the Admiral violated every regulation he vowed to uphold simply because he wanted to exploit your intellect." Just as quickly as he finished Khan was quick to retaliate in their verbal debate.

"Wanted to exploit my _savagery, _" Khan corrected turning to face Spock fully. "Intellect alone is useless in a fight Mr. Spock." He said with a look of growing confusion before it lifted. "You, you can't even break a rule how would you be expected to break, _bone. _He all but glared at Spock while somehow still maintaining a slightly blank mask while Spock watched him with dull acceptance.

"Marcus used me to design weapons," He continued turning his head to fix his eyes on Kirk, "To help him realize his vision of a militarized Starfleet, he sent _you _to use those weapons. To fire my torpedoes on an unsuspecting planet...and then he purposefully crippled your ship in enemy space, leading to one inevitable outcome." Walking towards Kirk he stopped, a small cruel smile on his face as the Captain watched him with uncertainty. Not sure whether he should believe the words he heard or not. "The Klingons would come searching for whomever was responsible, and you would have no chance at escape. Marcus, would finally have the war he talked about. The war he _always wanted_."

"No." Kirk replied immediately, refusing to believe that it could be even remotely true. "No. I watched you open fire in a room full of unarmed Starfleet officers you killed them in cold blood-" The Captain watched as Khan shook his head his eyes shut tightly before he swiftly turned around,

"Marcus," he hissed out. "Took my crew from me-"

"You are a _murderer_!" Kirk shouted refusing to listen. Unbeknownst to them they did not see Khan eyes fill with terror and pain until he snapped, biting each word like a savage dog would to a trespasser.

"He used my friends to control me." he stopped, trying in vain to reign in emotions he had only felt a long time ago, but it was too late. They had gained too much momentum and force from being suppressed for such a given amount of time for him to be able to control. Shuddering he stared at the white wall before him, not truly seeing it as familiar faces flashed into his head merging with the events he spoke of at the present and with events from way before. "I tried, to smuggle them to safety, by concealing them in the very weapons I had designed." He said quietly a hand raising up to cover his eyes, one arm crossing his chest as his shoulders hunched over faintly, until he took a deep yet choppy breath. Having lowered his arms back down to rest at his side he continued, his eyes still glassy as he fought the emotions battling within him. "But I was discovered...I had no choice, but to escape alone, and when I did, I had every reason to suspect that Marcus, had killed _every, single, one,_ of the people I hold most dear. So I responded in kind. My crew is my family Kirk, is there anything you would not do for your family?" His voice, broken with rage and grief as he turned to look at Kirk.

The entire room was silent, even those walking to and from the room from the start, for although they might not of heard what was said they seemed to sense that only silence would be excepted at that moment. Kirk remained staring at Khan with a stone like glare until the intercom sounded from overhead.

"Proximity alert, sir. There's a ship at warp heading right for us." Announced Sulu, efficiently ending the silence.

"Klingons?" The Captain questioned, taking the opportunity to look away from the broken man before him.

"At warp? Unlikely." Khan retorted returning to the spot where he originally was and sitting down, his back straight against the wall as he closed his eyes.

Kirk watched Khan for a moment before announcing, "Alert the ship to attend battle stations. If its nothing to worry about...then it was nothing to worry about."

"Yes, sir." Sulu answered before the alarms sounded signalling the Captain's decision.

"Let me help." Khan declared making Kirk flinch in surprise when he saw that the man was now standing and only inches from the glass.

Ignoring him Kirk towards the doors with a glance to Spock before walking away, the doors closed shut with a soft hiss behind both the Captain and his First Officer. Banging his fist against the glass in frustration he turned his back on the rest of the cabin, glaring heatedly at the walls before muttering softly, "Idiots...all of them...They're all idiots." he sighed quietly. His interest however perked at the sound of a person running. Spinning around on his heel all he was able to catch sight of was a flash of blue and blonde again, shouting managing to come through the doors before they shut. Seeing as he was once again alone, he sat, for isn't that what all men do when awaiting their deaths? They sit and watch it come, knowing that they can do nothing to stop it. Yet as he sat he felt the all too familiar rage began to claw beneath his skin, itching to be let out upon something, _anything._

* * *

He was running, running fast enough that it almost rivaled the speed he once ran at on a daily basis.

"_Captain! Captain, wait!_" He yelled, racing down the corridors. He saw both Kirk and Spock pause having heard his shouts, Kirk turning around fully while Spock simply looked over his shoulder.

"What is it? Speak quickly, I have a feeling that I will needed on the bridge." He said eyes landing on medical officer.

"Sir, let him help." he gasped out, barely managing to say the words coherently.

"Let who help?" the Captain asked confused by the sudden statement.

"Khan, he's not lying sir, he knows what he's doing." the man's eyes widened fractionally and he hurriedly added, "Not that you _don't _but he can help us sir!"

Kirk studied him a moment trying to place him to a name before giving up. "No."

"But sir!"

"No, that's my final answer." Kirk said firmly before turning back around and continuing down the hallway. Spock studied the man noting how is movements became less coordinated as he became desperate yet unwilling to bring up the subject again. Tilting his head he watched Kirk before calling out, "Captain!"

"What Spock?"

"I believe that it would be wise to listen to the officer, I feel that he knows something that we do not." he explained, his brow furrowing as he spoke. Kirk, his hands resting on his hips dropped his head as his eyes closing. Taking a deep breath and turned back around and stalked back over to the medical officer and Spock.

"Fine, but first, who are you?" Kirk demanded.

Wincing the officer replied. "Johne Harrison." defiantly he met the eyes of his Captain.

"Of course you are. Now explain to me why you feel that _Khan _can help us?" His anger surged at the officer's answer but had had enough and simply wanted an answer.

"Sir...I..." Johne shifted nervously before sighing, "Sir, I know Khan. If you give him the right motivation he will do anything you ask simply for the thrill of excitement he gets out of it." Johne opened his mouth as if to continue but quickly shut it after noticing both his Captain and superior officer's shocked expressions.

"Don't ask questions! Please." He begged hurriedly. "Just let me speak with him, you can even be in the same room with me. But let me just _talk _to him sir." he pleaded his cerulean eyes flicking uncertainly between Kirk and Spock.

"Fine. But we both expect answers to our questions by the end of it." Kirk said defeated. He has barely finished speaking before Johne was sprinting back down the corridor. With a quick look at Spock the both of them were soon quickly running after him.

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**So I hate leaving it there but I need to know whether or not this is good enough to finish. I was planning on this being a one shot but I didn't want to write all of it only to find out that everybody hated it. Reviews please if you want this continued! Oh, and yes Johne is another spelling of John...just in case I hadn't picked a close enough alternative spelling.**


	2. Chapter 2

**Alrighty then, so here's the next chapter. Depending on what you guys decide, I'm willing to continue you this until your all tired of it. The only things I feel that I should point out before you read is that I'm changing the story-line a little, there is going to probably be character OOCness {which I feel is a given seeing as how I didn't create or write the scripts for these characters}, and I'm changing some more things that I won't mention. But other than that, that's it!**

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**-Warning!-Needed Spoiler, that you should but don't have to read!- Johne Harrison and Khan's "moment/duet" is Pandora's Music Box by Nox Arcana. I'm not going to go into too much detail about it because it won't come out right. So it's probably in your best interest to listen to the song at some point.**

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They found him standing in front of the door with a hand frozen halfway to the control panel. There was a pained look in his eyes as he stared blankly ahead of him, until the sound of the Captain's and First Officer's slow footsteps drew him back into the present. Stiffly he turned and looked directly at Spock.

"Hypothetically, what would the chances of you ever forgiving the Captain if he faked his death and showed up a couple of years later?" he asked emotionless, his face unreadable yet cold at the same time.

Raising an eyebrow Spock glanced from Harrison, to the door, and finally to Kirk. Taking in a breath he thought for a moment before answering, "Roughly nine-teen point three percent." Spock watched as something broke in Harrison's eyes before he gave a curt nod and turned back to face the door.

"Right." he said, his posture not as straight as it had been. His built up confidence had started to crumble the moment he had asked the question. Eyes brightened as an idea popped into his head, he spun around, holding his hands in a placating gesture to the Captain.

"I'll um...be right back." he stammered out. But before he started to run off in the opposite direction he paused and turned back around again. Raising his hand he pointed at them before pointing to where they where standing. "Stay...There...please...sir. Don't move!" Having said what he felt he needed to he gave another nod, which was mostly to himself, he raced towards his quarters, slipping on the polished floors as he turned corners too fast. With his haste he almost missed his door, but even with his notice he had to stop his momentum by grabbing the edges of the almost non-existent door frame. Pressing the control panel with more force than was probably necessary, he darted in as soon as he could force himself through the door.

Johne stopped, his eyes scanning his room and trying to narrow down the possibilities of where he had placed his spare uniforms, from when he was still an ensign. Suddenly remembering he trotted towards his closet, then quickly sprang forward as a medium-sized object fell from the top shelf, having been dislodged from its resting place by him yanking the door open. Having caught it before it hit the floor he turned it over in his hands, studying it. Holding it in his left hand it laid comfortably along his form arm. There was a handle underneath it that made it less awkward to hold, it had a gentle curve at the opposite end that allowed him to bend his arm so that he could cradle it against his chest. His brow furrowed as he looked at its surface. It was a series of bumps that were barely separated from each other. At the end of each bump, closet to him, was a small opening. They were a beautiful silver color that had a teal blue tint to them, the thin board that they were resting on was the same teal color that, for some reason, seemed very dark. Intrigued Johne raised his right hand and tapped on of the bell-like bumps, in response a clear deep ringing sounded through the air.

His eyes widened before a choked sob caught in his throat. He remembered. It had been a gift, an outlet for his stress. Running his hand over the bells he bit his lips before realizing that he was here for a reason. Setting it carefully on his bed he darted back over to his closet, reaching as best he could he felt along the top shelf, hissing at the uncomfortable strain on his arm. He groaned when he felt the desired fabric at the tips of his fingers. Muttering angrily he spotted a small Tupperware storage container and, shuffling a little, he manage to place a foot on the box and launch himself up. Quickly grabbing the fabric he studied the two pieces before nodding, and changed with record timing. Taking a deep breath to reassure himself he smoothed down his uniform and grabbed the bells before taking off at a sprint to where he had left Kirk and Spock.

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Kirk was leaning against the wall next to the door when both he and Spock saw Harrison come back into view. As he skid to a halt in front of them with strange object cradled against his chest and a different uniform, all they could really do was stare at him. Spock snapped out of it first out of the both of them, "Officer, what are you holding? I do not think that I have seen it before."

Giving him a strained smile Harrison glanced at Spock before stroking the object tenderly, "It's a stress reliever, I never knew what it was called, never cared to be frank." He tapped one of the bell-like bumps thoughtfully before Kirk burst out.

"What the _hell _are you wearing?" he asked incredulously, his eyes flicking over the medical officer's new outfit.

Looking up slowly he met his Captains eyes, "I thought even _you_ would recognize a uniform when you saw one, sir." he stated sarcastically an eyebrow raised at the statement. But he figured the Captain did have a reason to be so bewildered, he had probably never seen the Star Fleet uniform that he was wearing. Mainly because, it was only the crew of the SS Botany Bay that was given these uniforms. The uniform, besides the pants, consisted of two pieces. The specified color of their duties was signified by a shirt that they were given, while the second was a pure black overcoat whose sleeves ended just above the wrist. It was a thick, heavy-duty, and high quality coat that each member of the crew treasured. On the right shoulder was a stripe that stretched from just behind the shoulder to a little under the collar-bone in a diagonal direction. The stripe was which ever color that particular officer was qualified under, and at the end of it was the traditional Star Fleet insignia, while the left shoulder had three bronze stars following the seam. The only other modification was the officer's color was in a solid band with a two inch width, approximately three inches from the end of the sleeve. The only person who had a differently styled uniform was the Captain, who had an entirely black outfit except for four silver-colored bands on the sleeves, two on each. Of course he also had the Star Fleet insignia and the three stars, but like the bands the stars were also silver.

Looking as though he had been scolded Kirk briefly ducked his head before it snapped up as Harrison started moving towards the door. Flinging his arm out he blocked the Medical Officer from the panel. With a quick look at Spock he said uncertainly, "How do we know we can trust you?"

With a sad smile Johne looked at the Captain, "Just watch." Raising his hand he gently moved Kirk's arm out-of-the-way and placed his hand a fraction of an inch away from the panel. Letting out a shaky breath he said quietly, "The both of you are going to enter first, I will follow, your steps are going to cover mine so he won't know I'm there. But whatever you do or whatever happens _do, not, say anything_. Understood?" he asked, his old commanding tone taking over his voice as his eyes did not leave the panel.

Both Kirk and Spock gave an affirmative nod before Johne opened the doors. Walking side by side the Captain and First Officer entered the room that they had left only an hour prior. They walked to the opposite edge of Khan's glass prison before stopping and turning to an angle where they could see both Khan and the officer. They watched as Johne looked from them to Khan meaningfully and got the hint that they were to watch the man in black instead of him. The man in question was sitting in the corner of the closed in area, his head resting against the two walls with his eyes closed. Had they not seen his body stiffen slightly upon their entrance they would have assumed that he was ignoring them, when in fact he was very much listening.

Kirk glanced over at Johne out of the corner of his eye and was slightly startled by what he saw. Harrison's head was bent over the object with his head tilted with concentration, his brow furrowed as he felt along the pieces of the instrument. He watched until he saw Harrison square his shoulders, determination flashing in eyes and took that as his cue to look back at Khan.

A steady yet slightly hasty melody suddenly broke the tense silence, and caused the Captain to jump. The bells, or what he assumed were bells, were being struck lightly and with an extreme amount of care as the pitch descended from its original high beginning before quickly starting over.

Intrigued the Captain watched Khan stiffen before he shuddered silently and hunched over. His hands coming up to tightly clutch his hair as if in pain. Which, the Captain decided, wouldn't be far from the truth judging by the mans white knuckles. He watched as the previously rage filled man began to shake, violently. Unable to help himself Kirk looked over at Spock who had a look of slowly dawning understanding as he watched the event unfold before him. After looking at the shaking man again he caught Harrison's eye again, trying his best to not worry a little for the man who had been hell bent on getting revenge.

Harrison shook his head slowly after keeping eye contact with Kirk for a few seemingly long moments. Having just changed tempo and notes the officer looked down briefly at the instrument before looking back at Kirk.

"_Watch_" he mouthed before returning his attention to Khan.

Kirk jumped in surprise as he felt Spock place his hand on his shoulder, while his eyes remained focused on Khan. It was only then that he realized that the psychopath was humming. A deep, bone shaking, hum that matched whatever tune the Medical Officer had and still was playing. The Captain hadn't realized it until Khan's accompaniment that the melody had such a dark personality to it, and yet, it held something. Some sort of meaning that was lost to him and yet fully understood by the two strange people performing it.

Kirk hadn't realized that his eyes were closing until they were shut firmly as he became enthralled in the sound around him. All at once he forgot that he was aboard the Enterprise, that he was standing in an interrogation room, that a ship was heading for them at warp, and that they were close enough to have gotten a proximity alert that had been announced over the intercom.

It turned out to be the moments of silence that brought Kirk back to reality, quickly followed by Spock tightening the grip on his shoulder as apparently he, too, was jerked into the present. As they forced themselves to focus again the picture before them took a few moments before it fully registered in their heads.

Khan was trembling even harder than he was before, tears now visible as the dripped slowly down his face and hit the floor with an inaudible sound. He was swaying too, a vague motion that only barely moved him from left to right while his hands remained fastened to his hair but not in the death like grip they had been before. His posture was more relaxed, in a way that was similar to a newly broken-spirited and exhausted stallion. His legs were apart with his knees bent, his elbows rested on his thighs as they remained rigidly locked in place, worst of all was that the man's head was lowered in such a visual of defeat that it even made the Captain's heart ache a slightly.

Kirk forced himself to watch for a few heartbeats before looking over at Harrison, hoping for an answer, and what he got sent his head spinning again. The Medical Officer had a fist firmly to his mouth a his body shook and lurched with silent sobs as his shoulders hunched over. Yet before his eyes the Captain watched as the officer before him took large breaths as his eyes slowly fluttered closed.

"Tell me _Captain_," the hoarse and broken tone made Kirk look back over at Khan. "Where did you learn that?" Kirk shivered at the trembling voice unsure whether it shook because of rage or grief as the prisoner remained still.

Nervously, Kirk looked over at Harrison who, in response, gave a slight shake of his head.

* * *

Bracing himself Harrison did his best not to fall to his knees at the sight the ruined creature before him. While at the same time he had to restrain himself from laughing at such a thought. Tilting his head he slowly started to speak.

"Once you rule out the impossible, whatever remains—however improbable—must be true." he started and as soon as he said it he felt pure, undiluted, agony start to filter its way into his heart.

"Let's just stick to the facts." he added, a slight hum starting to flit through his voice. The reaction he wanted came almost immediately.

"Stop." The word was said so hesitantly and yet with such a vast amount of hurt that it almost made Johne comply.

"I've always been able to keep myself distant. Divorce myself from feelings. But you see? Body's betraying me. Interesting, yes? Emotions. The grease on the lenses. The fly in the ointment." Harrison continued, forcing himself to keep pressing on. "I'm confident a star witness at a trial should come across as intelligent."

"_Stop_." The man in black had started to tremble again, except this time it seemed to be because of a mixture of fear as well as grief.

"I can open any door anywhere with a few tiny lines of computer code. No such thing as a private bank account now, they're all mine. No such thing as secrecy. I own secrecy. Nuclear codes. I could blow up NATO in alphabetical order. In a world of locked rooms, the man with the key is king, and honey, you should see me in a crown." He could feel his resolve starting to crumble the more he went on as his attempts at steeling himself against the prisoner became more frequent.

"_How_...How do you _know_ that?" It was said in the same tone as all of his other words before his question was, not only ignored, but almost covered up by Harrison as he started speaking again.

"Three bullets. Three gunmen. Three victims. There's no stopping them now. Unless my people see you jump. You can have me arrested, you can torture me. You can do anything you like with me, but nothing's going to prevent them from pulling the trigger. Your only three friends in the world will die. Unless—"

"_Please_!...Just, _stop_..." The pleaded words cut off Harrison.

There was a brief moment of silence before Harrison had the resolve to talk again.

"No, stay exactly where you are. Don't move. Keep your eyes fixed on me." Khan gave a soft whimper at the words,

"Please, will you do this for me?" Sentence barely understood through the choked sobs coming from the officer who spoke them. "Goodbye-"

"_No!_" The cry had such a desperate animalistic sound, that both Kirk and Spock retreated a few steps. Not knowing what to expect from the emotional being before him Spock inched his way in front of his Captain, his hand clenching as he forced himself to keep it by his side.

Having slammed into the glass as a result of his lunge Khan shuddered, the fiery seep of pain only dimly registered in his mind compared to the emotional breakdown that had been building up for years, only to break through his mental barricades now.

"Do you realize what you've done?" Johne asked, his voice shaking as he did his best to keep himself pulled together.

"I believe the correct question, is what have _you _done." Khan raised his head to be able to look at Johne his hands and knees on the floor, having paused in his motion to stand. As Khan's eyes landed on him Johne stiffened. For the eyes were filled with such a blood thirsty rage and hatred that Johne was afraid that the approach he had chosen was by far, the worst one he could have done.

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**Yes, yes, yes. I know its short but this has been on my computer ever since I posted the first chapter and figured you guys want story so. You know what? Here you go. Hopefully its not too choppy, but if there are places that I need the polish up let me know please. Also, I completely throwing the whole two-shot business out the window. I knew from the moment I started writing this that it was going to easily be a multi-chapter story. So, keeping up with the traditional Author's Notes, please Comment and Review please, I need it. Desperately. Oh! Almost forgot. I have an idea as to what I want the next chapter to be but I need ideas from you all, so that I can add more too it instead of just the bare minimum.**


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